PD5179 Sample Summary
## `summarise()` has grouped output by 'patient', 'age_at_sample_exact', 'age_at_sample', 'DOB', 'DATE_OF_DIAGNOSIS'. You can override using the `.groups` argument.
## Joining, by = "PDID"
|
|
patient
|
ID
|
age_at_sample_exact
|
cell_type
|
phase
|
BaitLabel
|
|
2
|
PD5179
|
PD5179c
|
35.44422
|
WGS
|
Recapture
|
c
|
|
3
|
PD5179
|
PD5179d
|
44.32854
|
WGS
|
Recapture
|
d
|
|
4
|
PD5179
|
PD5179e
|
48.79671
|
WGS
|
Recapture
|
e
|
|
1
|
PD5179
|
COLONY50
|
49.68104
|
BFU-E-Colony
|
Colony
|
NA
|
Tree
tree=plot_basic_tree(PD$pdx,label = PD$patient,style="classic")

Expanded Tree with Node Labels
The nodes in this plot can be cross-referenced with nodes specified in subsequent results. The plot also serves to give an idea of what the topology at the top of the tree looks like.
tree=plot_basic_tree(expand_short_branches(PD$pdx,prop = 0.1),label = PD$patient,style="classic")
node_labels(tree)

Timing of driver mutations (using Model = poisson_tree )
Note that the different colours on the tree indicate the separately fitted mutation rate clades. 
Driver Specific Mutation Rates & Telomere Lengths by Colony & Timepoint
##
## Random-Effects Model (k = 1; tau^2 estimator: REML)
##
## logLik deviance AIC BIC AICc
## -0.0000 0.0000 4.0000 -Inf 16.0000
##
## tau^2 (estimated amount of total heterogeneity): 0
## tau (square root of estimated tau^2 value): 0
## I^2 (total heterogeneity / total variability): 0.00%
## H^2 (total variability / sampling variability): 1.00
##
## Test for Heterogeneity:
## Q(df = 0) = 0.0000, p-val = 1.0000
##
## Model Results:
##
## estimate se zval pval ci.lb ci.ub
## 18.9207 0.7215 26.2223 <.0001 17.5065 20.3349 ***
##
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## `summarise()` has grouped output by 'patient'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'patient'. You can override using the `.groups` argument.
|
node
|
driver
|
status
|
child_count
|
type
|
colony_count
|
mean_lambda_rescaled
|
correction
|
sd_rescaled
|
lb_rescaled
|
ub_rescaled
|
median_rescaled
|
p_lt_wt
|
|
-1
|
WT
|
1
|
-1
|
local
|
3
|
18.92068
|
1.155211
|
0.5206336
|
17.93460
|
19.97831
|
18.90797
|
NA
|
|
97
|
JAK2,9+
|
1
|
89
|
local
|
6
|
23.39602
|
1.155211
|
1.1790889
|
21.49600
|
26.07115
|
23.24817
|
5.0e-05
|
|
98
|
1q+,9q-:JAK2,9+
|
1
|
83
|
local
|
83
|
23.58796
|
1.155211
|
1.2966562
|
21.36423
|
26.45578
|
23.47236
|
2.5e-05
|
Driver Acquisition Timeline
All ages are in terms of post conception years. The vertical red lines denote when colonies were sampled and blue lines when targeted follow up samples were taken.
|
patient
|
node
|
driver
|
child_count
|
lower_median
|
upper_median
|
lower_lb95
|
lower_ub95
|
upper_lb95
|
upper_ub95
|
N
|
group
|
age_at_diagnosis_pcy
|
max_age_at_sample
|
min_age_at_sample
|
|
PD5179
|
97
|
JAK2,9+
|
89
|
0.021439
|
20.47613
|
0.0117661
|
0.0466428
|
18.32146
|
23.47691
|
4
|
JAK2
|
34.77344
|
50.40931
|
36.17248
|
|
PD5179
|
180
|
1q+
|
6
|
20.476126
|
21.23976
|
18.3214562
|
23.4769087
|
19.10397
|
24.17348
|
4
|
1q+
|
34.77344
|
50.40931
|
36.17248
|
|
PD5179
|
98
|
1q+,9q-
|
83
|
20.476126
|
29.39066
|
18.3214562
|
23.4769087
|
27.34704
|
31.72855
|
4
|
1q+
|
34.77344
|
50.40931
|
36.17248
|
Summary of LOH timing inference
## Timings using the Clade Specific Rates
|
label
|
node
|
het.sensitivity
|
chr
|
start
|
end
|
nhet
|
nhom
|
mean_loh_event
|
lower_loh_event
|
upper_loh_event
|
t_before_end
|
t_before_end_lower
|
t_before_end_upper
|
kb
|
count_in_bin
|
count_se
|
pmut
|
pmut_se
|
xmean
|
xse_mean
|
xsd
|
x2.5.
|
x50.
|
x97.5.
|
xn_eff
|
xRhat
|
lmean
|
lse_mean
|
patient
|
driver3
|
child_count
|
|
9q-
|
181
|
0.9519
|
9
|
70484945
|
141112375
|
4
|
0
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
70700000
|
11349
|
106.5
|
0.02479
|
0.0002327
|
0.2265
|
0.001151
|
0.1704
|
0.008066
|
0.1907
|
0.6235
|
21938
|
0.9999
|
5.421
|
0.0003628
|
NA
|
NA
|
NA
|
Duplications?
## Timings using the Clade Specific Rates
|
label
|
node
|
het.sensitivity
|
chr
|
start
|
end
|
dupcount
|
ndupcount
|
mean_dup_event
|
lower_dup_event
|
upper_dup_event
|
t_before_end
|
t_before_end_lower
|
t_before_end_upper
|
kb
|
count_in_bin
|
count_se
|
pmut
|
pmut_se
|
xmean
|
xse_mean
|
xsd
|
x2.5.
|
x50.
|
x97.5.
|
xn_eff
|
xRhat
|
lmean
|
lse_mean
|
patient
|
driver3
|
child_count
|
|
1q+
|
98
|
0.9996
|
1
|
150000000
|
300000000
|
3
|
2
|
27.71
|
24.339
|
29.37
|
1.728
|
0.06013
|
5.094
|
99300000
|
15658
|
125.1
|
0.03420
|
0.0002733
|
0.8043
|
0.0010348
|
0.15600
|
0.4232
|
0.8425
|
0.9932
|
22726
|
1
|
5.646
|
0.0003342
|
PD5179
|
1q+,9q-:JAK2,9+
|
83
|
|
8+
|
182
|
0.9588
|
8
|
0
|
300000000
|
13
|
16
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
146400000
|
26546
|
162.9
|
0.05798
|
0.0003558
|
0.8504
|
0.0007159
|
0.09892
|
0.6276
|
0.8648
|
0.9916
|
19095
|
1
|
26.430
|
0.0012868
|
NA
|
NA
|
NA
|
|
9+
|
97
|
0.9999
|
9
|
0
|
300000000
|
6
|
19
|
10.54
|
5.232
|
16.41
|
10.061
|
4.18623
|
15.369
|
141300000
|
19318
|
139.0
|
0.04219
|
0.0003035
|
0.5111
|
0.0008728
|
0.13998
|
0.2531
|
0.5069
|
0.7966
|
25722
|
1
|
13.590
|
0.0006029
|
PD5179
|
JAK2,9+
|
89
|